What is the expected duplication rate for ATAC-seq data?

Duplicate reads are generally the result of PCR duplicates during library preparation, and in the pre-processing steps those reads are marked and removed. Since insertion of the Tn5 enzyme is random, PCR duplicates represent artifacts and can bias downstream analyses. A low duplication rate (< 5-10%) is optimal, and while slightly higher numbers are still acceptable (< 20-30%), higher percentages can suggest problems at the sample preparation step.